SMTL ID : 5ubb.1

Crystal structure of human alpha N-terminal protein methyltransferase 1B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 22 residues within 4Å: Chain A: Y.20, M.30, G.68, S.69, G.70, R.73, V.74, D.90, M.91, M.92, F.95, Y.116, S.117, L.118, Q.119, Q.134, W.135, V.136, H.139, L.140 Ligands: UNX.21, UNX.25 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.68, A:M.91, A:L.118, A:Q.119 Water bridges: A:V.74, A:S.117 Salt bridges: A:R.73 SAM.28: 22 residues within 4Å: Chain B: Y.20, M.30, G.68, S.69, G.70, R.73, V.74, D.90, M.91, M.92, F.95, Y.116, S.117, L.118, Q.119, Q.134, W.135, V.136, H.139, L.140 Ligands: UNX.48, UNX.52 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.68, B:M.91, B:L.118, B:Q.119 Water bridges: B:V.74, B:S.117 Salt bridges: B:R.73

52 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 1 residues within 4Å: Chain A: G.55 Ligand excluded by PLIP UNX.3: 3 residues within 4Å: Chain A: E.120, F.121, T.122 Ligand excluded by PLIP UNX.4: 2 residues within 4Å: Chain A: K.17, S.117 Ligand excluded by PLIP UNX.5: 2 residues within 4Å: Chain A: T.141, D.142 Ligand excluded by PLIP UNX.6: 2 residues within 4Å: Chain A: Q.46, K.47 Ligand excluded by PLIP UNX.7: 4 residues within 4Å: Chain A: N.167, V.182, T.183, R.184 Ligand excluded by PLIP UNX.8: 5 residues within 4Å: Chain A: W.135, V.136, S.137, G.138, D.166 Ligand excluded by PLIP UNX.9: 3 residues within 4Å: Chain A: M.91, M.92, E.93 Ligand excluded by PLIP UNX.10: 5 residues within 4Å: Chain A: G.57, R.58, A.59, N.159, I.161 Ligand excluded by PLIP UNX.11: 1 residues within 4Å: Chain A: E.9 Ligand excluded by PLIP UNX.12: 2 residues within 4Å: Chain A: F.34, W.135 Ligand excluded by PLIP UNX.13: 4 residues within 4Å: Chain A: R.126, R.153, D.154, L.156 Ligand excluded by PLIP UNX.14: 3 residues within 4Å: Chain A: Q.4, V.5, I.6 Ligand excluded by PLIP UNX.15: 6 residues within 4Å: Chain A: F.12, Y.13, A.16, H.139, S.180 Ligands: UNX.25 Ligand excluded by PLIP UNX.16: 5 residues within 4Å: Chain A: I.35, E.36, L.37, S.38, S.39 Ligand excluded by PLIP UNX.17: 2 residues within 4Å: Chain A: K.51, R.58 Ligand excluded by PLIP UNX.18: 2 residues within 4Å: Chain A: K.76, L.80 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Chain A: L.80, S.85, V.86 Ligand excluded by PLIP UNX.20: 4 residues within 4Å: Chain A: K.47, F.48, K.51, E.204 Ligand excluded by PLIP UNX.21: 6 residues within 4Å: Chain A: D.66, C.67, W.132, I.133, Q.134 Ligands: SAM.1 Ligand excluded by PLIP UNX.22: 1 residues within 4Å: Chain A: P.56 Ligand excluded by PLIP UNX.23: 4 residues within 4Å: Chain A: F.19, E.22, V.23 Ligands: UNX.24 Ligand excluded by PLIP UNX.24: 3 residues within 4Å: Chain A: F.19, V.23 Ligands: UNX.23 Ligand excluded by PLIP UNX.25: 5 residues within 4Å: Chain A: Y.13, A.16, H.139 Ligands: SAM.1, UNX.15 Ligand excluded by PLIP UNX.26: 4 residues within 4Å: Chain A: Q.11 Chain B: R.15, S.178 Ligands: UNX.27 Ligand excluded by PLIP UNX.27: 3 residues within 4Å: Chain A: Q.11 Chain B: R.15 Ligands: UNX.26 Ligand excluded by PLIP UNX.29: 1 residues within 4Å: Chain B: G.55 Ligand excluded by PLIP UNX.30: 3 residues within 4Å: Chain B: E.120, F.121, T.122 Ligand excluded by PLIP UNX.31: 2 residues within 4Å: Chain B: K.17, S.117 Ligand excluded by PLIP UNX.32: 2 residues within 4Å: Chain B: T.141, D.142 Ligand excluded by PLIP UNX.33: 2 residues within 4Å: Chain B: Q.46, K.47 Ligand excluded by PLIP UNX.34: 4 residues within 4Å: Chain B: N.167, V.182, T.183, R.184 Ligand excluded by PLIP UNX.35: 5 residues within 4Å: Chain B: W.135, V.136, S.137, G.138, D.166 Ligand excluded by PLIP UNX.36: 3 residues within 4Å: Chain B: M.91, M.92, E.93 Ligand excluded by PLIP UNX.37: 5 residues within 4Å: Chain B: G.57, R.58, A.59, N.159, I.161 Ligand excluded by PLIP UNX.38: 1 residues within 4Å: Chain B: E.9 Ligand excluded by PLIP UNX.39: 2 residues within 4Å: Chain B: F.34, W.135 Ligand excluded by PLIP UNX.40: 4 residues within 4Å: Chain B: R.126, R.153, D.154, L.156 Ligand excluded by PLIP UNX.41: 3 residues within 4Å: Chain B: Q.4, V.5, I.6 Ligand excluded by PLIP UNX.42: 6 residues within 4Å: Chain B: F.12, Y.13, A.16, H.139, S.180 Ligands: UNX.52 Ligand excluded by PLIP UNX.43: 5 residues within 4Å: Chain B: I.35, E.36, L.37, S.38, S.39 Ligand excluded by PLIP UNX.44: 2 residues within 4Å: Chain B: K.51, R.58 Ligand excluded by PLIP UNX.45: 2 residues within 4Å: Chain B: K.76, L.80 Ligand excluded by PLIP UNX.46: 3 residues within 4Å: Chain B: L.80, S.85, V.86 Ligand excluded by PLIP UNX.47: 4 residues within 4Å: Chain B: K.47, F.48, K.51, E.204 Ligand excluded by PLIP UNX.48: 6 residues within 4Å: Chain B: D.66, C.67, W.132, I.133, Q.134 Ligands: SAM.28 Ligand excluded by PLIP UNX.49: 1 residues within 4Å: Chain B: P.56 Ligand excluded by PLIP UNX.50: 4 residues within 4Å: Chain B: F.19, E.22, V.23 Ligands: UNX.51 Ligand excluded by PLIP UNX.51: 3 residues within 4Å: Chain B: F.19, V.23 Ligands: UNX.50 Ligand excluded by PLIP UNX.52: 5 residues within 4Å: Chain B: Y.13, A.16, H.139 Ligands: SAM.28, UNX.42 Ligand excluded by PLIP UNX.53: 4 residues within 4Å: Chain A: R.15, S.178 Chain B: Q.11 Ligands: UNX.54 Ligand excluded by PLIP UNX.54: 3 residues within 4Å: Chain A: R.15 Chain B: Q.11 Ligands: UNX.53 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, C. et al., An asparagine/glycine switch governs product specificity of human N-terminal methyltransferase NTMT2. Commun Biol (2018)

Release Date

2017-03-22

Peptides

Alpha N-terminal protein methyltransferase 1B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Alpha N-terminal protein methyltransferase 1B

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